Let's reminiscence about the greatness of ALTTP! Namely, small stuff you probably never did.
Grab one of the fishes that flop around on land near the water dungeon after you've drained the moat around it. If you carry that fish to the big lake to the right with all the octorocks and throw it in, it will thank you and give you some rupees. You can also schlep the fish to the merchant that sold you a bottle in the village.
Also, don't forget about the glittery good/gold bee that spawns when you tackle one of the statues inside a cave near the lake to the bottom right, where the ice rod is. The merchant will pay you some Rupees for it if you release it near him.
I love these little Easter eggs.